m@rtin_pseudomonas – Page 7 – Membrane Protein Biochemistry Lab

%7B%22status%22%3A%22success%22%2C%22updateneeded%22%3Afalse%2C%22instance%22%3Afalse%2C%22meta%22%3A%7B%22request_last%22%3A0%2C%22request_next%22%3A0%2C%22used_cache%22%3Atrue%7D%2C%22data%22%3A%5B%7B%22key%22%3A%22BTZTBTGM%22%2C%22library%22%3A%7B%22id%22%3A2503009%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Awotoro%20et%20al.%22%2C%22parsedDate%22%3A%222025-10-06%22%2C%22numChildren%22%3A0%7D%2C%22bib%22%3A%22%26lt%3Bdiv%20class%3D%26quot%3Bcsl-bib-body%26quot%3B%20style%3D%26quot%3Bline-height%3A%201.35%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%26quot%3B%26gt%3B%5Cn%20%20%26lt%3Bdiv%20class%3D%26quot%3Bcsl-entry%26quot%3B%26gt%3BAwotoro%2C%20E.%2C%20Ezekannagha%2C%20C.%2C%20Schwarz%2C%20F.%2C%20Tauscher%2C%20J.%2C%20Heider%2C%20D.%2C%20Ladewig%2C%20K.%2C%20Bon%2C%20C.L.%2C%20Moncoq%2C%20K.%2C%20Miroux%2C%20B.%2C%20Hattab%2C%20G.%2C%202025.%20MetaMP%3A%20Seamless%20Metadata%20Enrichment%20and%20AI%20Application%20Framework%20for%20Enhanced%20Membrane%20Protein%20Visualization%20and%20Analysis.%20%26lt%3Ba%20class%3D%26%23039%3Bzp-DOIURL%26%23039%3B%20href%3D%26%23039%3Bhttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.48550%5C%2FarXiv.2510.04776%26%23039%3B%26gt%3Bhttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.48550%5C%2FarXiv.2510.04776%26lt%3B%5C%2Fa%26gt%3B%26lt%3B%5C%2Fdiv%26gt%3B%5Cn%26lt%3B%5C%2Fdiv%26gt%3B%22%2C%22data%22%3A%7B%22itemType%22%3A%22preprint%22%2C%22title%22%3A%22MetaMP%3A%20Seamless%20Metadata%20Enrichment%20and%20AI%20Application%20Framework%20for%20Enhanced%20Membrane%20Protein%20Visualization%20and%20Analysis%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Ebenezer%22%2C%22lastName%22%3A%22Awotoro%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Chisom%22%2C%22lastName%22%3A%22Ezekannagha%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Florian%22%2C%22lastName%22%3A%22Schwarz%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Johannes%22%2C%22lastName%22%3A%22Tauscher%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Dominik%22%2C%22lastName%22%3A%22Heider%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Katharina%22%2C%22lastName%22%3A%22Ladewig%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Christel%20Le%22%2C%22lastName%22%3A%22Bon%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Karine%22%2C%22lastName%22%3A%22Moncoq%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Bruno%22%2C%22lastName%22%3A%22Miroux%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Georges%22%2C%22lastName%22%3A%22Hattab%22%7D%5D%2C%22abstractNote%22%3A%22Structural%20biology%20has%20made%20significant%20progress%20in%20determining%20membrane%20proteins%2C%20leading%20to%20a%20remarkable%20increase%20in%20the%20number%20of%20available%20structures%20in%20dedicated%20databases.%20The%20inherent%20complexity%20of%20membrane%20protein%20structures%2C%20coupled%20with%20challenges%20such%20as%20missing%20data%2C%20inconsistencies%2C%20and%20computational%20barriers%20from%20disparate%20sources%2C%20underscores%20the%20need%20for%20improved%20database%20integration.%20To%20address%20this%20gap%2C%20we%20present%20MetaMP%2C%20a%20framework%20that%20unifies%20membrane-protein%20databases%20within%20a%20web%20application%20and%20uses%20machine%20learning%20for%20classification.%20MetaMP%20improves%20data%20quality%20by%20enriching%20metadata%2C%20offering%20a%20user-friendly%20interface%2C%20and%20providing%20eight%20interactive%20views%20for%20streamlined%20exploration.%20MetaMP%20was%20effective%20across%20tasks%20of%20varying%20difficulty%2C%20demonstrating%20advantages%20across%20different%20levels%20without%20compromising%20speed%20or%20accuracy%2C%20according%20to%20user%20evaluations.%20Moreover%2C%20MetaMP%20supports%20essential%20functions%20such%20as%20structure%20classification%20and%20outlier%20detection.%20We%20present%20three%20practical%20applications%20of%20Artificial%20Intelligence%20%28AI%29%20in%20membrane%20protein%20research%3A%20predicting%20transmembrane%20segments%2C%20reconciling%20legacy%20databases%2C%20and%20classifying%20structures%20with%20explainable%20AI%20support.%20In%20a%20validation%20focused%20on%20statistics%2C%20MetaMP%20resolved%2077%25%20of%20data%20discrepancies%20and%20accurately%20predicted%20the%20class%20of%20newly%20identified%20membrane%20proteins%2098%25%20of%20the%20time%20and%20overtook%20expert%20curation.%20Altogether%2C%20MetaMP%20is%20a%20much-needed%20resource%20that%20harmonizes%20current%20knowledge%20and%20empowers%20AI-driven%20exploration%20of%20membrane-protein%20architecture.%22%2C%22genre%22%3A%22%22%2C%22repository%22%3A%22arXiv%22%2C%22archiveID%22%3A%22arXiv%3A2510.04776%22%2C%22date%22%3A%222025-10-06%22%2C%22DOI%22%3A%2210.48550%5C%2FarXiv.2510.04776%22%2C%22citationKey%22%3A%22%22%2C%22url%22%3A%22http%3A%5C%2F%5C%2Farxiv.org%5C%2Fabs%5C%2F2510.04776%22%2C%22language%22%3A%22%22%2C%22collections%22%3A%5B%2263TU6NVS%22%5D%2C%22dateModified%22%3A%222025-11-24T10%3A22%3A22Z%22%7D%7D%2C%7B%22key%22%3A%22PQNBQIB4%22%2C%22library%22%3A%7B%22id%22%3A2503009%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Fourel%20et%20al.%22%2C%22parsedDate%22%3A%222025-06-27%22%2C%22numChildren%22%3A0%7D%2C%22bib%22%3A%22%26lt%3Bdiv%20class%3D%26quot%3Bcsl-bib-body%26quot%3B%20style%3D%26quot%3Bline-height%3A%201.35%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%26quot%3B%26gt%3B%5Cn%20%20%26lt%3Bdiv%20class%3D%26quot%3Bcsl-entry%26quot%3B%26gt%3BFourel%2C%20C.%2C%20Gautier%2C%20Y.%2C%20Pozza%2C%20A.%2C%20Giraud%2C%20F.%2C%20Point%2C%20E.%2C%20Bon%2C%20C.L.%2C%20Moncoq%2C%20K.%2C%20Stirnemann%2C%20G.%2C%20H%26%23xE9%3Bnin%2C%20J.%2C%20Lescop%2C%20E.%2C%20Catoire%2C%20L.J.%2C%202025.%20Allosteric%20coupling%20between%20a%20lipid%20bilayer%20and%20a%20membrane%20protein.%20Biophysical%20Journal%200.%20%26lt%3Ba%20class%3D%26%23039%3Bzp-DOIURL%26%23039%3B%20href%3D%26%23039%3Bhttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1016%5C%2Fj.bpj.2025.06.033%26%23039%3B%26gt%3Bhttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1016%5C%2Fj.bpj.2025.06.033%26lt%3B%5C%2Fa%26gt%3B%26lt%3B%5C%2Fdiv%26gt%3B%5Cn%26lt%3B%5C%2Fdiv%26gt%3B%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22Allosteric%20coupling%20between%20a%20lipid%20bilayer%20and%20a%20membrane%20protein%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Clarisse%22%2C%22lastName%22%3A%22Fourel%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Yanna%22%2C%22lastName%22%3A%22Gautier%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Alexandre%22%2C%22lastName%22%3A%22Pozza%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Fran%5Cu00e7ois%22%2C%22lastName%22%3A%22Giraud%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Elodie%22%2C%22lastName%22%3A%22Point%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Christel%20Le%22%2C%22lastName%22%3A%22Bon%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Karine%22%2C%22lastName%22%3A%22Moncoq%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Guillaume%22%2C%22lastName%22%3A%22Stirnemann%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22J%5Cu00e9r%5Cu00f4me%22%2C%22lastName%22%3A%22H%5Cu00e9nin%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Ewen%22%2C%22lastName%22%3A%22Lescop%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Laurent%20J.%22%2C%22lastName%22%3A%22Catoire%22%7D%5D%2C%22abstractNote%22%3A%22%22%2C%22date%22%3A%222025-06-27%22%2C%22section%22%3A%22%22%2C%22partNumber%22%3A%22%22%2C%22partTitle%22%3A%22%22%2C%22DOI%22%3A%2210.1016%5C%2Fj.bpj.2025.06.033%22%2C%22citationKey%22%3A%22%22%2C%22url%22%3A%22https%3A%5C%2F%5C%2Fwww.cell.com%5C%2Fbiophysj%5C%2Fabstract%5C%2FS0006-3495%2825%2900410-2%22%2C%22PMID%22%3A%2240581816%22%2C%22PMCID%22%3A%22%22%2C%22ISSN%22%3A%220006-3495%2C%201542-0086%22%2C%22language%22%3A%22English%22%2C%22collections%22%3A%5B%2263TU6NVS%22%5D%2C%22dateModified%22%3A%222025-07-28T08%3A58%3A36Z%22%7D%7D%2C%7B%22key%22%3A%22LQ837KEZ%22%2C%22library%22%3A%7B%22id%22%3A2503009%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Lesur%20et%20al.%22%2C%22parsedDate%22%3A%222025-03-01%22%2C%22numChildren%22%3A0%7D%2C%22bib%22%3A%22%26lt%3Bdiv%20class%3D%26quot%3Bcsl-bib-body%26quot%3B%20style%3D%26quot%3Bline-height%3A%201.35%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%26quot%3B%26gt%3B%5Cn%20%20%26lt%3Bdiv%20class%3D%26quot%3Bcsl-entry%26quot%3B%26gt%3BLesur%2C%20E.%2C%20Zhang%2C%20Y.%2C%20Dautin%2C%20N.%2C%20Dietrich%2C%20C.%2C%20Sierra-Gallay%2C%20I.L.%20de%20la%2C%20Augusto%2C%20L.A.%2C%20Rollando%2C%20P.%2C%20Lazar%2C%20N.%2C%20Urban%2C%20D.%2C%20Doisneau%2C%20G.%2C%20Constantinesco-Becker%2C%20F.%2C%20Tilbeurgh%2C%20H.V.%2C%20Guianvarc%26%23x2019%3Bh%2C%20D.%2C%20Bourdreux%2C%20Y.%2C%20Bayan%2C%20N.%2C%202025.%20Synthetic%20mycolates%20derivatives%20to%20decipher%20protein%20mycoloylation%2C%20a%20unique%20post-translational%20modification%20in%20bacteria.%20Journal%20of%20Biological%20Chemistry%20301.%20%26lt%3Ba%20class%3D%26%23039%3Bzp-DOIURL%26%23039%3B%20href%3D%26%23039%3Bhttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1016%5C%2Fj.jbc.2025.108243%26%23039%3B%26gt%3Bhttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1016%5C%2Fj.jbc.2025.108243%26lt%3B%5C%2Fa%26gt%3B%26lt%3B%5C%2Fdiv%26gt%3B%5Cn%26lt%3B%5C%2Fdiv%26gt%3B%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22Synthetic%20mycolates%20derivatives%20to%20decipher%20protein%20mycoloylation%2C%20a%20unique%20post-translational%20modification%20in%20bacteria%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Emilie%22%2C%22lastName%22%3A%22Lesur%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Yijie%22%2C%22lastName%22%3A%22Zhang%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Nathalie%22%2C%22lastName%22%3A%22Dautin%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Christiane%22%2C%22lastName%22%3A%22Dietrich%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Ines%20Li%20de%20la%22%2C%22lastName%22%3A%22Sierra-Gallay%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Luis%20A.%22%2C%22lastName%22%3A%22Augusto%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Paulin%22%2C%22lastName%22%3A%22Rollando%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Noureddine%22%2C%22lastName%22%3A%22Lazar%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Dominique%22%2C%22lastName%22%3A%22Urban%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Gilles%22%2C%22lastName%22%3A%22Doisneau%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Florence%22%2C%22lastName%22%3A%22Constantinesco-Becker%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Herman%20Van%22%2C%22lastName%22%3A%22Tilbeurgh%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Dominique%22%2C%22lastName%22%3A%22Guianvarc%27h%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Yann%22%2C%22lastName%22%3A%22Bourdreux%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Nicolas%22%2C%22lastName%22%3A%22Bayan%22%7D%5D%2C%22abstractNote%22%3A%22%26lt%3Bp%26gt%3BProtein%20mycoloylation%20is%20a%20newly%20characterized%20post-translational%20modification%20%28PTM%29%20specifically%20found%20in%20%26lt%3Bi%26gt%3BCorynebacteriales%26lt%3B%5C%2Fi%26gt%3B%2C%20an%20order%20of%20bacteria%20that%20includes%20numerous%20human%20pathogens.%20Their%20envelope%20is%20composed%20of%20a%20unique%20outer%20membrane%2C%20the%20so-called%20mycomembrane%20made%20of%20very-long%20chain%20fatty%20acids%2C%20named%20mycolic%20acids.%20Recently%2C%20some%20mycomembrane%20proteins%20including%20PorA%20have%20been%20unambiguously%20shown%20to%20be%20covalently%20modified%20with%20mycolic%20acids%20in%20the%20model%20organism%20%26lt%3Bi%26gt%3BCorynebacterium%20glutamicum%26lt%3B%5C%2Fi%26gt%3B%20by%20a%20mechanism%20that%20relies%20on%20the%20mycoloyltransferase%20MytC.%20This%20PTM%20represents%20the%20first%20example%20of%20protein%20%26lt%3Bi%26gt%3BO%26lt%3B%5C%2Fi%26gt%3B-acylation%20in%20prokaryotes%20and%20the%20first%20example%20of%20protein%20modification%20by%20mycolic%20acid.%20Through%20the%20design%20and%20synthesis%20of%20trehalose%20monomycolate%20%28TMM%29%20analogs%2C%20we%20prove%20that%20%26lt%3Bi%26gt%3Bi%26lt%3B%5C%2Fi%26gt%3B%29%20MytC%20is%20the%20mycoloyltransferase%20directly%20involved%20in%20this%20PTM%2C%20%26lt%3Bi%26gt%3Bii%26lt%3B%5C%2Fi%26gt%3B%29%20TMM%2C%20but%20not%20trehalose%20dimycolate%20%28TDM%29%2C%20is%20a%20suitable%20mycolate%20donor%20for%20PorA%20mycoloylation%2C%20%26lt%3Bi%26gt%3Biii%26lt%3B%5C%2Fi%26gt%3B%29%20MytC%20is%20able%20to%20discriminate%20between%20an%20acyl%20and%20a%20mycoloyl%20chain%20%26lt%3Bi%26gt%3Bin%20vitro%26lt%3B%5C%2Fi%26gt%3B%20unlike%20other%20trehalose%20mycoloyltransferases.%20We%20also%20solved%20the%20structure%20of%20MytC%20acyl-enzyme%20obtained%20with%20a%20soluble%20short%20TMM%20analogs%20which%20constitutes%20the%20first%20mycoloyltransferase%20structure%20covalently%20linked%20to%20an%20authentic%20mycolic%20acid%20moiety.%20These%20data%20highlight%20the%20great%20conformational%20flexibility%20of%20the%20active%20site%20of%20MytC%20during%20the%20reaction%20cycle%20and%20pave%20the%20way%20for%20a%20better%20understanding%20of%20the%20catalytic%20mechanism%20of%20all%20members%20of%20the%20mycoloyltransferase%20family%20including%20the%20essential%20Antigen85%20enzymes%20in%20%26lt%3Bi%26gt%3BMycobacteria%26lt%3B%5C%2Fi%26gt%3B.%26lt%3B%5C%2Fp%26gt%3B%22%2C%22date%22%3A%222025%5C%2F03%5C%2F01%22%2C%22section%22%3A%22%22%2C%22partNumber%22%3A%22%22%2C%22partTitle%22%3A%22%22%2C%22DOI%22%3A%2210.1016%5C%2Fj.jbc.2025.108243%22%2C%22citationKey%22%3A%22%22%2C%22url%22%3A%22%22%2C%22PMID%22%3A%2239880088%22%2C%22PMCID%22%3A%22%22%2C%22ISSN%22%3A%220021-9258%2C%201083-351X%22%2C%22language%22%3A%22English%22%2C%22collections%22%3A%5B%2263TU6NVS%22%5D%2C%22dateModified%22%3A%222025-08-07T08%3A42%3A32Z%22%7D%7D%5D%7D

Awotoro, E., Ezekannagha, C., Schwarz, F., Tauscher, J., Heider, D., Ladewig, K., Bon, C.L., Moncoq, K., Miroux, B., Hattab, G., 2025. MetaMP: Seamless Metadata Enrichment and AI Application Framework for Enhanced Membrane Protein Visualization and Analysis. https://doi.org/10.48550/arXiv.2510.04776

Fourel, C., Gautier, Y., Pozza, A., Giraud, F., Point, E., Bon, C.L., Moncoq, K., Stirnemann, G., Hénin, J., Lescop, E., Catoire, L.J., 2025. Allosteric coupling between a lipid bilayer and a membrane protein. Biophysical Journal 0. https://doi.org/10.1016/j.bpj.2025.06.033

Lesur, E., Zhang, Y., Dautin, N., Dietrich, C., Sierra-Gallay, I.L. de la, Augusto, L.A., Rollando, P., Lazar, N., Urban, D., Doisneau, G., Constantinesco-Becker, F., Tilbeurgh, H.V., Guianvarc’h, D., Bourdreux, Y., Bayan, N., 2025. Synthetic mycolates derivatives to decipher protein mycoloylation, a unique post-translational modification in bacteria. Journal of Biological Chemistry 301. https://doi.org/10.1016/j.jbc.2025.108243